Field of Science

Defending 'functional design' analysis at Evo-WIBO

In a couple of weeks I'll be giving a short talk at the regional Evo-WIBO meeting.  My title is What's an evolutionary biologist doing in a physics lab?.  I think I'm going to combine a description of my specific scientific question (the physical properties of DNA uptake by Haemophilus influenzae) with a rehash of the defense of 'functional design' that I made in a post last month.  So I might subtitle the talk A defense of functional design analysis.

I'll only have 15 minutes including question time, so I'll need to keep it simple.
  • The simple answer is, I'm measuring the physical properties of DNA uptake by the bacterium Haemophilus influenzae.  I'll show you how this is done at the end of my talk, with a nice explanatory animation.
  • Why is this of evolutionary interest? Because it's one of the final pieces of the Do bacteria have sex? puzzle.
  • Why aren't I using more evolution-style approaches, behaving like a proper evolutionary biologist?  How will knowing physical forces answer evolutionary questions?  Shouldn't I be using the comparative method?  Since these are bacteria, why aren't I doing Rich Lenski-style lab evolution experiments?
  • A defense of 'functional design' analysis:
  • Understanding 'natural history' (the stamp collecting side of biology?) is fundamental to investigating evolutionary forces.  Before we try to explain how natural selection has acted on any phenotype or behaviour, we first need a solid understanding of what the phenotype or behaviour is.
  • First a big-organism example: The head-nodding lizards.  We can use the usual methods of natural history.  What does it do, when does it do it, what are the typical outcomes?
  • Next, a bacterial example: For bacteria, we need to use the methods of molecular biology.  Consider RecBCD (3 proteins that work together).  How was it discovered, what was its function initially thought to be?  What was later learned about the phenomenon (not by evolutionary biologists).  Molecular biologists often treat both 'functions' as equivalently important.  How should evolutionary biologists think about it (consider relative strengths of selective forces).
  • Similar history of thinking about nearly all the genes that contribute to homologous recombination in bacteria.  The molecular biology isn't my work, but I spell out the implications for evolutionary biologists.
  • Main conclusion:  Many (and perhaps all) bacteria don't have 'sex'; that is, they don't have any genes that evolved to promote homologous recombination with alleles from other cells of the same or closely related species.  Two of the three processes that move DNA from one cell to another are caused by genetic parasites, and the genes responsible for the physical recombination all have important functions in DNA replication and repair.  True of E. coli.
  • I say 'perhaps all' because the function of one of the three processes that move DNA is still controversial.  That's natural competence

1 comment:

  1. Thoughts concerning your upcoming talk at Evo-WIBO... (BTW, the 'Shift Happens' T-shirts are great!)....

    Why do you need a "big organism" example? I'd save the time - but you know this audience better than I.

    But that isn't why I chose to write - what I'm really curious about is the sense I get that you feel a phenotype must be some sort of evolutionary goal (i.e., why would we have an a priori expectation that enzymes would evolve to accomplish homologous recombination?) Gender doesn't seem to pop onto the Natural History landscape full blown and ready to be appreciated. So why should HR? I really like the notion that HR might proceed from a DNA replication and repair background.

    And is it not possible that natural competence is currently an orphan process that exists for food uptake but was once a piece of a primordial sex process that developed further in other lineages but was cast aside in bacteria? (photosynthesis may have been cast aside in oomycetes in favor of parasitism).

    To me, HR has to be more beneficial than horizontal gene transfer for a lineage to find it worth the trouble. When organisms are extremely simple the selective disadvantage of maintaining DNA that isn't carrying its weight should lead to its elimination. The notion of an allele implies the existence of a gene - but a gene not in the sense of a capable ORF but in the sense of two or more ORFs in a population that perform the same function in manner that the environment will influence and that selection can act on. If said variant ORFs come to be in the same cell, then HR can go to work on them.

    The value of taking a different tack on a problem is prescient. And physics offers a host of tools and a philosophical background that could really help. To me the challenge of the 15 minute presentation is to illustrate how having data that describe the physical process of DNA uptake should allow mathematical model development for the process which then allows development of testable hypotheses. There are "big organism" examples of this approach bearing fruit.


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